Pseudotime heatmaps of significant transcription factors
q value < 5*10^-5
significant_genes_q_value_5_10_minus_5 <- filter(diff_test_res_all_genes, qval < 5*10^-5) %>% .$gene
cat("Number of significant genes: ", length(significant_genes_q_value_5_10_minus_5))
## Number of significant genes: 4390
significant_transcription_factors_q_value_5_10_minus_5 <- as.character(significant_genes_q_value_5_10_minus_5[significant_genes_q_value_5_10_minus_5 %in% transcription_factors$Symbol])
cat("Number of significant transcription factors:", length(significant_transcription_factors_q_value_5_10_minus_5))
## Number of significant transcription factors: 260
plot_genes_heatmap_output_q_value_5_10_minus_5 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], cluster_rows=TRUE, num_clusters=3, return_heatmap=TRUE, show_rownames = TRUE)

plot_genes_heatmap_output_q_value_5_10_minus_5 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], cluster_rows=TRUE, num_clusters=1, return_heatmap=TRUE, show_rownames = TRUE)

# The RMarkdown PDF has issues, hence this custom function to save the PDF file.
save_pheatmap_pdf(plot_genes_heatmap_output_q_value_5_10_minus_5[[2]], file.path("figures", "1-hindbrain_oligodendrocytes_joint_pons_clusters_14_4_8_21", "diff_test_res_plots_transcription_factors_only_q_value_5_10_minus_5_heatmap_custom.pdf"), width=16, height=36)
## pdf
## 2
heatmap_matrix_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[1]]
ph_res_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[2]]
pheatmap_ordering_q_value_5_10_minus_5 <- rownames(heatmap_matrix_q_value_5_10_minus_5[ph_res_q_value_5_10_minus_5$tree_row[["order"]],])
transcription_factors_table_q_value_5_10_minus_5 <- filter(diff_test_res_all_genes, gene %in% significant_transcription_factors_q_value_5_10_minus_5)
# Put genes from the transcription factor table in the same order
transcription_factors_table_q_value_5_10_minus_5 <- transcription_factors_table_q_value_5_10_minus_5 %>% arrange(match(gene, pheatmap_ordering_q_value_5_10_minus_5))
write.table(transcription_factors_table_q_value_5_10_minus_5, file.path(tables_directory, "1-hindbrain_oligodendrocytes_joint_pons_clusters_14_4_8_21-significant_transcription_factors_diff_test_analysis_qval_5_10_minus_5.txt"), sep="\t", quote=FALSE, row.names=FALSE)
heatmap_matrix_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[1]]
heatmap_matrix_q_value_5_10_minus_5 <- as.data.frame(heatmap_matrix_q_value_5_10_minus_5) %>% rownames_to_column("gene")
heatmap_matrix_q_value_5_10_minus_5 <- heatmap_matrix_q_value_5_10_minus_5 %>% arrange(match(gene, pheatmap_ordering_q_value_5_10_minus_5))
heatmap_matrix_q_value_5_10_minus_5 %>% head(20) %>% kable() %>% kable_styling() %>% scroll_box(height="200px", width="600px")
|
gene
|
1
|
2
|
3
|
4
|
5
|
6
|
7
|
8
|
9
|
10
|
11
|
12
|
13
|
14
|
15
|
16
|
17
|
18
|
19
|
20
|
21
|
22
|
23
|
24
|
25
|
26
|
27
|
28
|
29
|
30
|
31
|
32
|
33
|
34
|
35
|
36
|
37
|
38
|
39
|
40
|
41
|
42
|
43
|
44
|
45
|
46
|
47
|
48
|
49
|
50
|
51
|
52
|
53
|
54
|
55
|
56
|
57
|
58
|
59
|
60
|
61
|
62
|
63
|
64
|
65
|
66
|
67
|
68
|
69
|
70
|
71
|
72
|
73
|
74
|
75
|
76
|
77
|
78
|
79
|
80
|
81
|
82
|
83
|
84
|
85
|
86
|
87
|
88
|
89
|
90
|
91
|
92
|
93
|
94
|
95
|
96
|
97
|
98
|
99
|
100
|
|
Zfpm1
|
-1.2712856
|
-1.2592238
|
-1.2468984
|
-1.2343038
|
-1.2214343
|
-1.2082843
|
-1.1948479
|
-1.1811192
|
-1.1670921
|
-1.1527605
|
-1.1381181
|
-1.1231585
|
-1.1078752
|
-1.0922616
|
-1.0763109
|
-1.0600163
|
-1.0433707
|
-1.0263671
|
-1.0089982
|
-0.9912567
|
-0.9731351
|
-0.9546257
|
-0.9357207
|
-0.9164123
|
-0.8966925
|
-0.8765531
|
-0.8559857
|
-0.8349820
|
-0.8135333
|
-0.7916310
|
-0.7692661
|
-0.7464296
|
-0.7231123
|
-0.6993051
|
-0.6749983
|
-0.6501823
|
-0.6248475
|
-0.5989839
|
-0.5725813
|
-0.5456296
|
-0.5181184
|
-0.4900371
|
-0.4613751
|
-0.4321215
|
-0.4022695
|
-0.3718164
|
-0.3407603
|
-0.3090997
|
-0.2768340
|
-0.2439630
|
-0.2104875
|
-0.1764087
|
-0.1417289
|
-0.1064509
|
-0.0705787
|
-0.0341168
|
0.0029292
|
0.0405526
|
0.0787459
|
0.1175005
|
0.1568067
|
0.1966539
|
0.2370301
|
0.2779222
|
0.3193159
|
0.3611957
|
0.4035467
|
0.4463674
|
0.4896640
|
0.5334429
|
0.5777112
|
0.6224765
|
0.6677468
|
0.7135307
|
0.7598376
|
0.8066771
|
0.8540596
|
0.9019962
|
0.9504985
|
0.9995789
|
1.0492504
|
1.099527
|
1.150422
|
1.201952
|
1.254132
|
1.306980
|
1.360512
|
1.414748
|
1.469705
|
1.525406
|
1.581870
|
1.639120
|
1.697179
|
1.756071
|
1.815821
|
1.8764546
|
1.9380000
|
2.0004854
|
2.0639402
|
2.1283954
|
|
Thra
|
-1.1413348
|
-1.1296662
|
-1.1179384
|
-1.1061447
|
-1.0942781
|
-1.0823315
|
-1.0702978
|
-1.0581695
|
-1.0459394
|
-1.0335997
|
-1.0211429
|
-1.0085611
|
-0.9958464
|
-0.9829907
|
-0.9699858
|
-0.9568235
|
-0.9434952
|
-0.9299923
|
-0.9163061
|
-0.9024277
|
-0.8883481
|
-0.8740582
|
-0.8595485
|
-0.8448096
|
-0.8298319
|
-0.8146055
|
-0.7991205
|
-0.7833668
|
-0.7673340
|
-0.7510117
|
-0.7343892
|
-0.7174557
|
-0.7002001
|
-0.6826111
|
-0.6646775
|
-0.6463874
|
-0.6277292
|
-0.6086908
|
-0.5892598
|
-0.5694239
|
-0.5491704
|
-0.5284862
|
-0.5073583
|
-0.4857728
|
-0.4637050
|
-0.4411185
|
-0.4179759
|
-0.3942389
|
-0.3698684
|
-0.3448244
|
-0.3190661
|
-0.2925516
|
-0.2652383
|
-0.2370825
|
-0.2080394
|
-0.1780634
|
-0.1471075
|
-0.1151238
|
-0.0820633
|
-0.0478755
|
-0.0125091
|
0.0240888
|
0.0619722
|
0.1011965
|
0.1418184
|
0.1838960
|
0.2274833
|
0.2725913
|
0.3192087
|
0.3673233
|
0.4169220
|
0.4679904
|
0.5205131
|
0.5744736
|
0.6298538
|
0.6866347
|
0.7447955
|
0.8043142
|
0.8651673
|
0.9273298
|
0.9907751
|
1.055475
|
1.121400
|
1.188519
|
1.256799
|
1.326205
|
1.396702
|
1.468252
|
1.540817
|
1.614354
|
1.688823
|
1.764181
|
1.840381
|
1.917379
|
1.995127
|
2.0735751
|
2.1526746
|
2.2323739
|
2.3126211
|
2.3933629
|
|
Zfp579
|
-0.7810556
|
-0.7882617
|
-0.7953880
|
-0.8024058
|
-0.8092868
|
-0.8160039
|
-0.8225304
|
-0.8288404
|
-0.8349087
|
-0.8407104
|
-0.8462215
|
-0.8514181
|
-0.8562766
|
-0.8607738
|
-0.8648867
|
-0.8685922
|
-0.8718672
|
-0.8746884
|
-0.8770323
|
-0.8788748
|
-0.8801914
|
-0.8809569
|
-0.8811451
|
-0.8807290
|
-0.8796802
|
-0.8779689
|
-0.8755640
|
-0.8724324
|
-0.8685389
|
-0.8638462
|
-0.8583146
|
-0.8519013
|
-0.8445604
|
-0.8362429
|
-0.8268957
|
-0.8164615
|
-0.8048785
|
-0.7920798
|
-0.7779927
|
-0.7625387
|
-0.7456323
|
-0.7271808
|
-0.7070830
|
-0.6852317
|
-0.6615676
|
-0.6360868
|
-0.6087878
|
-0.5796703
|
-0.5487360
|
-0.5159894
|
-0.4814388
|
-0.4450975
|
-0.4069842
|
-0.3671247
|
-0.3255522
|
-0.2823090
|
-0.2374465
|
-0.1910271
|
-0.1431246
|
-0.0938250
|
-0.0432274
|
0.0085550
|
0.0613950
|
0.1151501
|
0.1696626
|
0.2247594
|
0.2802654
|
0.3361074
|
0.3922668
|
0.4487271
|
0.5054737
|
0.5624937
|
0.6197763
|
0.6773126
|
0.7350960
|
0.7931216
|
0.8513870
|
0.9098916
|
0.9686373
|
1.0276280
|
1.0868700
|
1.146372
|
1.206143
|
1.266198
|
1.326552
|
1.387221
|
1.448225
|
1.509587
|
1.571331
|
1.633482
|
1.696071
|
1.759127
|
1.822684
|
1.886777
|
1.951445
|
2.0167275
|
2.0826663
|
2.1493062
|
2.2166940
|
2.2848790
|
|
Zfp740
|
-0.7565998
|
-0.7659481
|
-0.7752028
|
-0.7843304
|
-0.7932980
|
-0.8020737
|
-0.8106264
|
-0.8189256
|
-0.8269414
|
-0.8346448
|
-0.8420071
|
-0.8490002
|
-0.8555964
|
-0.8617681
|
-0.8674882
|
-0.8727297
|
-0.8774653
|
-0.8816681
|
-0.8853107
|
-0.8883653
|
-0.8908039
|
-0.8925979
|
-0.8937177
|
-0.8941331
|
-0.8938127
|
-0.8927241
|
-0.8908332
|
-0.8881045
|
-0.8845008
|
-0.8799827
|
-0.8745086
|
-0.8680345
|
-0.8605136
|
-0.8518960
|
-0.8421283
|
-0.8311537
|
-0.8189111
|
-0.8053350
|
-0.7903550
|
-0.7738951
|
-0.7558738
|
-0.7362029
|
-0.7147871
|
-0.6915263
|
-0.6663750
|
-0.6393484
|
-0.6104647
|
-0.5797433
|
-0.5472049
|
-0.5128730
|
-0.4767742
|
-0.4389391
|
-0.3994034
|
-0.3582082
|
-0.3154011
|
-0.2710369
|
-0.2251784
|
-0.1778970
|
-0.1292737
|
-0.0793994
|
-0.0283762
|
0.0236828
|
0.0766523
|
0.1303949
|
0.1847600
|
0.2395843
|
0.2947046
|
0.3500587
|
0.4056378
|
0.4614351
|
0.5174451
|
0.5736640
|
0.6300896
|
0.6867212
|
0.7435601
|
0.8006089
|
0.8578722
|
0.9153564
|
0.9730693
|
1.0310210
|
1.0892231
|
1.147689
|
1.206435
|
1.265477
|
1.324835
|
1.384531
|
1.444586
|
1.505027
|
1.565881
|
1.627176
|
1.688943
|
1.751216
|
1.814031
|
1.877423
|
1.941434
|
2.0061038
|
2.0714773
|
2.1376005
|
2.2045215
|
2.2722913
|
|
Tmf1
|
-0.6616883
|
-0.6782612
|
-0.6947307
|
-0.7110485
|
-0.7271672
|
-0.7430397
|
-0.7586198
|
-0.7738616
|
-0.7887199
|
-0.8031500
|
-0.8171077
|
-0.8305492
|
-0.8434311
|
-0.8557102
|
-0.8673439
|
-0.8782894
|
-0.8885045
|
-0.8979467
|
-0.9065738
|
-0.9143435
|
-0.9212131
|
-0.9271401
|
-0.9320813
|
-0.9359934
|
-0.9388325
|
-0.9405539
|
-0.9411124
|
-0.9404620
|
-0.9385556
|
-0.9353451
|
-0.9307812
|
-0.9248133
|
-0.9173893
|
-0.9084555
|
-0.8979563
|
-0.8858343
|
-0.8720299
|
-0.8564813
|
-0.8391243
|
-0.8198918
|
-0.7987141
|
-0.7755182
|
-0.7502281
|
-0.7227671
|
-0.6931308
|
-0.6613905
|
-0.6276212
|
-0.5918985
|
-0.5542992
|
-0.5149015
|
-0.4737853
|
-0.4310327
|
-0.3867283
|
-0.3409593
|
-0.2938159
|
-0.2453916
|
-0.1957836
|
-0.1450925
|
-0.0934230
|
-0.0408838
|
0.0124121
|
0.0663475
|
0.1208005
|
0.1756451
|
0.2307503
|
0.2859808
|
0.3412081
|
0.3963916
|
0.4515355
|
0.5066448
|
0.5617250
|
0.6167820
|
0.6718224
|
0.7268530
|
0.7818815
|
0.8369157
|
0.8919640
|
0.9470356
|
1.0021396
|
1.0572862
|
1.1124855
|
1.167749
|
1.223087
|
1.278511
|
1.334035
|
1.389671
|
1.445431
|
1.501330
|
1.557382
|
1.613600
|
1.670001
|
1.726600
|
1.783412
|
1.840453
|
1.897741
|
1.9552933
|
2.0131266
|
2.0712595
|
2.1297105
|
2.1884986
|
|
Tcf7l2
|
-0.7576342
|
-0.7685488
|
-0.7793482
|
-0.7899945
|
-0.8004512
|
-0.8106825
|
-0.8206538
|
-0.8303315
|
-0.8396827
|
-0.8486755
|
-0.8572786
|
-0.8654616
|
-0.8731943
|
-0.8804472
|
-0.8871911
|
-0.8933971
|
-0.8990362
|
-0.9040795
|
-0.9084979
|
-0.9122619
|
-0.9153415
|
-0.9177061
|
-0.9193241
|
-0.9201630
|
-0.9201890
|
-0.9193666
|
-0.9176590
|
-0.9150271
|
-0.9114300
|
-0.9068239
|
-0.9011626
|
-0.8943969
|
-0.8864741
|
-0.8773380
|
-0.8669282
|
-0.8551802
|
-0.8420247
|
-0.8273872
|
-0.8111877
|
-0.7933402
|
-0.7737525
|
-0.7523252
|
-0.7289517
|
-0.7035205
|
-0.6759823
|
-0.6463572
|
-0.6146704
|
-0.5809504
|
-0.5452296
|
-0.5075459
|
-0.4679431
|
-0.4264722
|
-0.3831919
|
-0.3381697
|
-0.2914822
|
-0.2432159
|
-0.1934676
|
-0.1423448
|
-0.0899661
|
-0.0364610
|
0.0180298
|
0.0733545
|
0.1293506
|
0.1858448
|
0.2426540
|
0.2995852
|
0.3564507
|
0.4131731
|
0.4697330
|
0.5261141
|
0.5823027
|
0.6382873
|
0.6940594
|
0.7496126
|
0.8049428
|
0.8600482
|
0.9149293
|
0.9695886
|
1.0240306
|
1.0782619
|
1.1322907
|
1.186127
|
1.239783
|
1.293273
|
1.346610
|
1.399813
|
1.452899
|
1.505887
|
1.558798
|
1.611656
|
1.664481
|
1.717301
|
1.770139
|
1.823023
|
1.875980
|
1.9290392
|
1.9822300
|
2.0355831
|
2.0891296
|
2.1429020
|
|
Bbx
|
-0.9798442
|
-0.9786615
|
-0.9774545
|
-0.9761993
|
-0.9748721
|
-0.9734489
|
-0.9719057
|
-0.9702186
|
-0.9683632
|
-0.9663155
|
-0.9640509
|
-0.9615450
|
-0.9587732
|
-0.9557106
|
-0.9523320
|
-0.9486124
|
-0.9445259
|
-0.9400469
|
-0.9351490
|
-0.9298056
|
-0.9239899
|
-0.9176741
|
-0.9108305
|
-0.9034303
|
-0.8954444
|
-0.8868428
|
-0.8775951
|
-0.8676697
|
-0.8570344
|
-0.8456558
|
-0.8334998
|
-0.8205309
|
-0.8067127
|
-0.7920071
|
-0.7763750
|
-0.7597757
|
-0.7421669
|
-0.7235046
|
-0.7037430
|
-0.6828342
|
-0.6607285
|
-0.6373738
|
-0.6127157
|
-0.5866988
|
-0.5593054
|
-0.5305577
|
-0.5004803
|
-0.4690984
|
-0.4364381
|
-0.4025264
|
-0.3673916
|
-0.3310635
|
-0.2935734
|
-0.2549544
|
-0.2152417
|
-0.1744723
|
-0.1326857
|
-0.0899239
|
-0.0462313
|
-0.0016553
|
0.0437540
|
0.0899434
|
0.1368566
|
0.1844340
|
0.2326127
|
0.2813262
|
0.3305104
|
0.3801469
|
0.4302402
|
0.4807951
|
0.5318168
|
0.5833105
|
0.6352815
|
0.6877352
|
0.7406774
|
0.7941140
|
0.8480508
|
0.9024941
|
0.9574503
|
1.0129257
|
1.0689272
|
1.125462
|
1.182536
|
1.240158
|
1.298334
|
1.357072
|
1.416381
|
1.476268
|
1.536741
|
1.597808
|
1.659480
|
1.721763
|
1.784668
|
1.848203
|
1.912378
|
1.9772033
|
2.0426880
|
2.1088426
|
2.1756774
|
2.2432031
|
|
Tulp4
|
-0.9739800
|
-0.9756105
|
-0.9772083
|
-0.9787412
|
-0.9801774
|
-0.9814850
|
-0.9826321
|
-0.9835870
|
-0.9843178
|
-0.9847926
|
-0.9849796
|
-0.9848469
|
-0.9843625
|
-0.9834941
|
-0.9822097
|
-0.9804766
|
-0.9782621
|
-0.9755333
|
-0.9722570
|
-0.9683993
|
-0.9639263
|
-0.9588033
|
-0.9529954
|
-0.9464666
|
-0.9391809
|
-0.9311009
|
-0.9221888
|
-0.9124058
|
-0.9017122
|
-0.8900672
|
-0.8774288
|
-0.8637538
|
-0.8489976
|
-0.8331145
|
-0.8160568
|
-0.7977755
|
-0.7782195
|
-0.7573362
|
-0.7350706
|
-0.7113658
|
-0.6861626
|
-0.6593991
|
-0.6310111
|
-0.6009341
|
-0.5691600
|
-0.5357413
|
-0.5007339
|
-0.4641955
|
-0.4261856
|
-0.3867657
|
-0.3459997
|
-0.3039540
|
-0.2606978
|
-0.2163036
|
-0.1708468
|
-0.1244064
|
-0.0770650
|
-0.0289088
|
0.0199720
|
0.0694835
|
0.1195276
|
0.1700020
|
0.2208005
|
0.2718126
|
0.3229239
|
0.3740157
|
0.4249751
|
0.4757665
|
0.5263932
|
0.5768597
|
0.6271711
|
0.6773335
|
0.7273532
|
0.7772378
|
0.8269951
|
0.8766339
|
0.9261635
|
0.9755940
|
1.0249360
|
1.0742010
|
1.1234008
|
1.172548
|
1.221656
|
1.270739
|
1.319811
|
1.368887
|
1.417983
|
1.467115
|
1.516300
|
1.565555
|
1.614899
|
1.664349
|
1.713926
|
1.763648
|
1.813536
|
1.8636103
|
1.9138929
|
1.9644052
|
2.0151697
|
2.0662093
|
|
Lcorl
|
0.0145057
|
-0.0450676
|
-0.1034902
|
-0.1606718
|
-0.2165299
|
-0.2709894
|
-0.3239823
|
-0.3754475
|
-0.4253302
|
-0.4735819
|
-0.5201599
|
-0.5650264
|
-0.6081490
|
-0.6494991
|
-0.6890524
|
-0.7267879
|
-0.7626872
|
-0.7967348
|
-0.8289165
|
-0.8592198
|
-0.8876328
|
-0.9141441
|
-0.9387417
|
-0.9614131
|
-0.9821441
|
-1.0009189
|
-1.0177189
|
-1.0325227
|
-1.0453050
|
-1.0560364
|
-1.0646824
|
-1.0712031
|
-1.0755519
|
-1.0776756
|
-1.0775128
|
-1.0749936
|
-1.0700384
|
-1.0625569
|
-1.0524474
|
-1.0395950
|
-1.0238712
|
-1.0051317
|
-0.9832156
|
-0.9579490
|
-0.9292719
|
-0.8972501
|
-0.8619533
|
-0.8234515
|
-0.7818178
|
-0.7371312
|
-0.6894788
|
-0.6389584
|
-0.5856807
|
-0.5297715
|
-0.4713741
|
-0.4106506
|
-0.3477842
|
-0.2829802
|
-0.2164676
|
-0.1484999
|
-0.0793557
|
-0.0093391
|
0.0612199
|
0.1319666
|
0.2025213
|
0.2724810
|
0.3414505
|
0.4092648
|
0.4758820
|
0.5412684
|
0.6053973
|
0.6682492
|
0.7298115
|
0.7900781
|
0.8490493
|
0.9067315
|
0.9631371
|
1.0182839
|
1.0721953
|
1.1248998
|
1.1764305
|
1.226825
|
1.276127
|
1.324382
|
1.371641
|
1.417957
|
1.463389
|
1.507999
|
1.551850
|
1.595010
|
1.637549
|
1.679541
|
1.721061
|
1.762187
|
1.803001
|
1.8435852
|
1.8840248
|
1.9244073
|
1.9648223
|
2.0053614
|
|
Zfp516
|
-0.2383464
|
-0.2803540
|
-0.3212084
|
-0.3608676
|
-0.3992963
|
-0.4364655
|
-0.4723517
|
-0.5069366
|
-0.5402064
|
-0.5721515
|
-0.6027659
|
-0.6320468
|
-0.6599939
|
-0.6866091
|
-0.7118961
|
-0.7358599
|
-0.7585066
|
-0.7798424
|
-0.7998741
|
-0.8186078
|
-0.8360493
|
-0.8522033
|
-0.8670733
|
-0.8806608
|
-0.8929655
|
-0.9039848
|
-0.9137129
|
-0.9221412
|
-0.9292575
|
-0.9350453
|
-0.9394839
|
-0.9425477
|
-0.9442052
|
-0.9444192
|
-0.9431457
|
-0.9403330
|
-0.9359213
|
-0.9298415
|
-0.9220145
|
-0.9123496
|
-0.9007435
|
-0.8870787
|
-0.8712221
|
-0.8530263
|
-0.8324120
|
-0.8093782
|
-0.7839222
|
-0.7560386
|
-0.7257204
|
-0.6929614
|
-0.6577579
|
-0.6201110
|
-0.5800283
|
-0.5375268
|
-0.4926346
|
-0.4453935
|
-0.3958615
|
-0.3441153
|
-0.2902525
|
-0.2343947
|
-0.1766893
|
-0.1173122
|
-0.0564698
|
0.0055993
|
0.0686220
|
0.1322906
|
0.1962851
|
0.2604586
|
0.3247586
|
0.3891368
|
0.4535486
|
0.5179535
|
0.5823152
|
0.6466016
|
0.7107854
|
0.7748440
|
0.8387596
|
0.9025194
|
0.9661159
|
1.0295464
|
1.0928139
|
1.155926
|
1.218897
|
1.281746
|
1.344496
|
1.407177
|
1.469824
|
1.532479
|
1.595187
|
1.658000
|
1.720975
|
1.784175
|
1.847668
|
1.911528
|
1.975835
|
2.0406741
|
2.1061368
|
2.1723202
|
2.2393276
|
2.3072684
|
|
Dach2
|
-0.2867327
|
-0.3362488
|
-0.3839235
|
-0.4297318
|
-0.4736593
|
-0.5157015
|
-0.5558619
|
-0.5941516
|
-0.6305879
|
-0.6651935
|
-0.6979954
|
-0.7290238
|
-0.7583118
|
-0.7858941
|
-0.8118067
|
-0.8360857
|
-0.8587673
|
-0.8798866
|
-0.8994775
|
-0.9175719
|
-0.9341994
|
-0.9493866
|
-0.9631570
|
-0.9755302
|
-0.9865214
|
-0.9961415
|
-1.0043957
|
-1.0112839
|
-1.0167995
|
-1.0209289
|
-1.0236513
|
-1.0249369
|
-1.0247471
|
-1.0230329
|
-1.0197338
|
-1.0147765
|
-1.0080734
|
-0.9995208
|
-0.9889968
|
-0.9763587
|
-0.9614404
|
-0.9440490
|
-0.9239608
|
-0.9009215
|
-0.8747562
|
-0.8453882
|
-0.8127374
|
-0.7767192
|
-0.7372485
|
-0.6942445
|
-0.6476353
|
-0.5973637
|
-0.5433927
|
-0.4857124
|
-0.4243463
|
-0.3593585
|
-0.2908616
|
-0.2190235
|
-0.1440755
|
-0.0663186
|
0.0138692
|
0.0960280
|
0.1796115
|
0.2639843
|
0.3484210
|
0.4321079
|
0.5141978
|
0.5942034
|
0.6718484
|
0.7468826
|
0.8190823
|
0.8882513
|
0.9542217
|
1.0168544
|
1.0760389
|
1.1316932
|
1.1837632
|
1.2322219
|
1.2770683
|
1.3183262
|
1.3560429
|
1.390288
|
1.421150
|
1.448738
|
1.473177
|
1.494609
|
1.513187
|
1.529079
|
1.542461
|
1.553520
|
1.562450
|
1.569452
|
1.574730
|
1.578495
|
1.580959
|
1.5823369
|
1.5828447
|
1.5826999
|
1.5821200
|
1.5813227
|
|
Mitf
|
-0.8963212
|
-0.8989518
|
-0.9015411
|
-0.9040715
|
-0.9065258
|
-0.9088877
|
-0.9111412
|
-0.9132710
|
-0.9152618
|
-0.9170989
|
-0.9187679
|
-0.9202541
|
-0.9215434
|
-0.9226212
|
-0.9234729
|
-0.9240836
|
-0.9244378
|
-0.9245194
|
-0.9243118
|
-0.9237973
|
-0.9229569
|
-0.9217705
|
-0.9202163
|
-0.9182709
|
-0.9159085
|
-0.9131012
|
-0.9098181
|
-0.9060254
|
-0.9016854
|
-0.8967568
|
-0.8911932
|
-0.8849433
|
-0.8779496
|
-0.8701481
|
-0.8614667
|
-0.8518247
|
-0.8411315
|
-0.8292846
|
-0.8161687
|
-0.8016534
|
-0.7855909
|
-0.7678139
|
-0.7481318
|
-0.7263310
|
-0.7022373
|
-0.6757323
|
-0.6466964
|
-0.6150085
|
-0.5805491
|
-0.5432031
|
-0.5028637
|
-0.4594369
|
-0.4128462
|
-0.3630375
|
-0.3099856
|
-0.2536999
|
-0.1942312
|
-0.1316783
|
-0.0661949
|
0.0020037
|
0.0726347
|
0.1453418
|
0.2196914
|
0.2951687
|
0.3711767
|
0.4470367
|
0.5220302
|
0.5957084
|
0.6677843
|
0.7379917
|
0.8060859
|
0.8718461
|
0.9350766
|
0.9956076
|
1.0532964
|
1.1080270
|
1.1597109
|
1.2082859
|
1.2537159
|
1.2959901
|
1.3351218
|
1.371147
|
1.404124
|
1.434129
|
1.461259
|
1.485627
|
1.507362
|
1.526604
|
1.543509
|
1.558241
|
1.570973
|
1.581889
|
1.591175
|
1.599027
|
1.605641
|
1.6112202
|
1.6159686
|
1.6200928
|
1.6238010
|
1.6273027
|
|
Foxn3
|
-0.5506148
|
-0.5806278
|
-0.6104213
|
-0.6399189
|
-0.6690452
|
-0.6977267
|
-0.7258907
|
-0.7534663
|
-0.7803837
|
-0.8065741
|
-0.8319701
|
-0.8565051
|
-0.8801135
|
-0.9027305
|
-0.9242921
|
-0.9447348
|
-0.9639956
|
-0.9820117
|
-0.9987206
|
-1.0140599
|
-1.0279668
|
-1.0403784
|
-1.0512313
|
-1.0604615
|
-1.0680039
|
-1.0737926
|
-1.0777603
|
-1.0798382
|
-1.0799558
|
-1.0780405
|
-1.0740178
|
-1.0678103
|
-1.0593380
|
-1.0485179
|
-1.0352636
|
-1.0194848
|
-1.0010875
|
-0.9799729
|
-0.9560379
|
-0.9291738
|
-0.8992666
|
-0.8661962
|
-0.8298361
|
-0.7900593
|
-0.7468848
|
-0.7004864
|
-0.6510473
|
-0.5987545
|
-0.5437996
|
-0.4863798
|
-0.4266989
|
-0.3649682
|
-0.3014072
|
-0.2362438
|
-0.1697156
|
-0.1020699
|
-0.0335642
|
0.0355335
|
0.1049448
|
0.1743803
|
0.2435402
|
0.3121141
|
0.3797816
|
0.4462123
|
0.5110668
|
0.5739971
|
0.6346766
|
0.6930123
|
0.7490306
|
0.8027632
|
0.8542465
|
0.9035209
|
0.9506310
|
0.9956253
|
1.0385555
|
1.0794772
|
1.1184491
|
1.1555327
|
1.1907926
|
1.2242959
|
1.2561124
|
1.286314
|
1.314975
|
1.342172
|
1.367981
|
1.392485
|
1.415762
|
1.437898
|
1.458974
|
1.479077
|
1.498294
|
1.516711
|
1.534418
|
1.551503
|
1.568057
|
1.5841706
|
1.5999354
|
1.6154437
|
1.6307885
|
1.6460631
|
|
Ebf2
|
-0.7522794
|
-0.7534545
|
-0.7545397
|
-0.7555390
|
-0.7564566
|
-0.7572970
|
-0.7580649
|
-0.7587649
|
-0.7594015
|
-0.7599790
|
-0.7605016
|
-0.7609733
|
-0.7613977
|
-0.7617782
|
-0.7621180
|
-0.7624199
|
-0.7626864
|
-0.7629199
|
-0.7631221
|
-0.7632949
|
-0.7634395
|
-0.7635569
|
-0.7636477
|
-0.7637125
|
-0.7637510
|
-0.7637629
|
-0.7637473
|
-0.7637028
|
-0.7636273
|
-0.7635183
|
-0.7633721
|
-0.7631842
|
-0.7629490
|
-0.7626590
|
-0.7623052
|
-0.7618760
|
-0.7613567
|
-0.7607288
|
-0.7599685
|
-0.7590456
|
-0.7579211
|
-0.7565443
|
-0.7548492
|
-0.7527491
|
-0.7501399
|
-0.7468984
|
-0.7428713
|
-0.7378670
|
-0.7316482
|
-0.7239228
|
-0.7143333
|
-0.7024465
|
-0.6877426
|
-0.6696062
|
-0.6473184
|
-0.6200555
|
-0.5868928
|
-0.5468209
|
-0.4987742
|
-0.4416795
|
-0.3745240
|
-0.2964488
|
-0.2068662
|
-0.1055982
|
0.0069700
|
0.1297349
|
0.2608337
|
0.3984130
|
0.5406185
|
0.6853564
|
0.8303594
|
0.9732654
|
1.1117002
|
1.2433611
|
1.3660960
|
1.4779729
|
1.5773392
|
1.6628653
|
1.7335736
|
1.7888512
|
1.8284476
|
1.852459
|
1.861300
|
1.855669
|
1.836502
|
1.804928
|
1.762219
|
1.709743
|
1.648921
|
1.581181
|
1.507928
|
1.430513
|
1.350206
|
1.268181
|
1.185503
|
1.1031218
|
1.0218689
|
0.9424582
|
0.8654917
|
0.7914658
|
|
Hmgxb3
|
-1.1506975
|
-1.1492093
|
-1.1476889
|
-1.1461063
|
-1.1444311
|
-1.1426326
|
-1.1406801
|
-1.1385424
|
-1.1361882
|
-1.1335856
|
-1.1307024
|
-1.1275056
|
-1.1239620
|
-1.1200374
|
-1.1156967
|
-1.1109042
|
-1.1056227
|
-1.0998140
|
-1.0934386
|
-1.0864552
|
-1.0788210
|
-1.0704910
|
-1.0614182
|
-1.0515531
|
-1.0408435
|
-1.0292341
|
-1.0166665
|
-1.0030785
|
-0.9884037
|
-0.9725716
|
-0.9555064
|
-0.9371271
|
-0.9173465
|
-0.8960709
|
-0.8731994
|
-0.8486229
|
-0.8222237
|
-0.7938740
|
-0.7634356
|
-0.7307582
|
-0.6956786
|
-0.6580190
|
-0.6175860
|
-0.5741733
|
-0.5276835
|
-0.4781472
|
-0.4256117
|
-0.3701387
|
-0.3118070
|
-0.2507156
|
-0.1869868
|
-0.1207692
|
-0.0522406
|
0.0183892
|
0.0908759
|
0.1649378
|
0.2402541
|
0.3164635
|
0.3931622
|
0.4699041
|
0.5462007
|
0.6215217
|
0.6952971
|
0.7669196
|
0.8357486
|
0.9011150
|
0.9623703
|
1.0192178
|
1.0715586
|
1.1193244
|
1.1624757
|
1.2010008
|
1.2349150
|
1.2642591
|
1.2890977
|
1.3095180
|
1.3256281
|
1.3375549
|
1.3454424
|
1.3494500
|
1.3497506
|
1.346529
|
1.339978
|
1.330301
|
1.317707
|
1.302408
|
1.284622
|
1.264565
|
1.242458
|
1.218519
|
1.192963
|
1.166005
|
1.137854
|
1.108716
|
1.078792
|
1.0482775
|
1.0173617
|
0.9862282
|
0.9550542
|
0.9240108
|
|
Zfp488
|
-0.5745624
|
-0.6086374
|
-0.6421171
|
-0.6749232
|
-0.7069824
|
-0.7382266
|
-0.7685916
|
-0.7980180
|
-0.8264500
|
-0.8538353
|
-0.8801250
|
-0.9052729
|
-0.9292353
|
-0.9519706
|
-0.9734387
|
-0.9936009
|
-1.0124194
|
-1.0298567
|
-1.0458752
|
-1.0604369
|
-1.0735027
|
-1.0850323
|
-1.0949832
|
-1.1033104
|
-1.1099662
|
-1.1148987
|
-1.1180523
|
-1.1193663
|
-1.1187742
|
-1.1162034
|
-1.1115740
|
-1.1047981
|
-1.0957786
|
-1.0844085
|
-1.0705694
|
-1.0541304
|
-1.0349465
|
-1.0128574
|
-0.9876853
|
-0.9592333
|
-0.9272829
|
-0.8915921
|
-0.8518921
|
-0.8078930
|
-0.7594707
|
-0.7066928
|
-0.6496434
|
-0.5884198
|
-0.5231368
|
-0.4539322
|
-0.3809715
|
-0.3044527
|
-0.2246109
|
-0.1417233
|
-0.0561129
|
0.0318477
|
0.1217326
|
0.2130604
|
0.3052919
|
0.3978295
|
0.4900171
|
0.5811413
|
0.6704338
|
0.7570753
|
0.8402008
|
0.9189063
|
0.9923182
|
1.0600529
|
1.1220012
|
1.1780936
|
1.2282975
|
1.2726161
|
1.3110859
|
1.3437753
|
1.3707825
|
1.3922327
|
1.4082765
|
1.4190870
|
1.4248576
|
1.4257998
|
1.4221408
|
1.414121
|
1.401991
|
1.386012
|
1.366451
|
1.343580
|
1.317674
|
1.289009
|
1.257863
|
1.224508
|
1.189218
|
1.152259
|
1.113894
|
1.074379
|
1.033964
|
0.9928908
|
0.9513944
|
0.9097007
|
0.8680276
|
0.8265845
|
|
Elf1
|
-0.6961644
|
-0.7208353
|
-0.7449734
|
-0.7685213
|
-0.7914264
|
-0.8136407
|
-0.8351204
|
-0.8558259
|
-0.8757206
|
-0.8947717
|
-0.9129487
|
-0.9302237
|
-0.9465709
|
-0.9619659
|
-0.9763857
|
-0.9898078
|
-1.0022103
|
-1.0135713
|
-1.0238681
|
-1.0330774
|
-1.0411743
|
-1.0481320
|
-1.0539215
|
-1.0585110
|
-1.0618648
|
-1.0639438
|
-1.0647038
|
-1.0640954
|
-1.0620631
|
-1.0585447
|
-1.0534699
|
-1.0467597
|
-1.0383253
|
-1.0280667
|
-1.0158711
|
-1.0016120
|
-0.9851465
|
-0.9663141
|
-0.9449339
|
-0.9208022
|
-0.8936895
|
-0.8633370
|
-0.8294530
|
-0.7917148
|
-0.7499230
|
-0.7040297
|
-0.6539983
|
-0.5998026
|
-0.5414324
|
-0.4789000
|
-0.4122466
|
-0.3415492
|
-0.2669276
|
-0.1885514
|
-0.1066471
|
-0.0215048
|
0.0665158
|
0.1569797
|
0.2493720
|
0.3430946
|
0.4374646
|
0.5317137
|
0.6249908
|
0.7163657
|
0.8048359
|
0.8893357
|
0.9688128
|
1.0427266
|
1.1108351
|
1.1729502
|
1.2289355
|
1.2787053
|
1.3222220
|
1.3594945
|
1.3905755
|
1.4155581
|
1.4345734
|
1.4477865
|
1.4553935
|
1.4576177
|
1.4547066
|
1.446928
|
1.434566
|
1.417921
|
1.397300
|
1.373021
|
1.345406
|
1.314779
|
1.281462
|
1.245779
|
1.208045
|
1.168571
|
1.127661
|
1.085609
|
1.042698
|
0.9992034
|
0.9553856
|
0.9114949
|
0.8677689
|
0.8244328
|
|
Sox10
|
-1.2928045
|
-1.2824160
|
-1.2719922
|
-1.2615040
|
-1.2509225
|
-1.2402188
|
-1.2293638
|
-1.2183283
|
-1.2070830
|
-1.1955987
|
-1.1838458
|
-1.1717949
|
-1.1594164
|
-1.1466805
|
-1.1335575
|
-1.1200173
|
-1.1060299
|
-1.0915651
|
-1.0765926
|
-1.0610819
|
-1.0450023
|
-1.0283231
|
-1.0110132
|
-0.9930415
|
-0.9743768
|
-0.9549873
|
-0.9348413
|
-0.9139069
|
-0.8921517
|
-0.8695434
|
-0.8460491
|
-0.8216358
|
-0.7962701
|
-0.7699184
|
-0.7425468
|
-0.7141209
|
-0.6846060
|
-0.6539672
|
-0.6221690
|
-0.5891756
|
-0.5549507
|
-0.5194577
|
-0.4826593
|
-0.4445207
|
-0.4050669
|
-0.3643851
|
-0.3225660
|
-0.2797010
|
-0.2358823
|
-0.1912029
|
-0.1457565
|
-0.0996378
|
-0.0529426
|
-0.0057673
|
0.0417906
|
0.0896324
|
0.1376589
|
0.1857696
|
0.2338630
|
0.2818369
|
0.3295878
|
0.3770116
|
0.4240030
|
0.4704562
|
0.5162641
|
0.5613191
|
0.6055229
|
0.6488580
|
0.6913474
|
0.7330146
|
0.7738835
|
0.8139783
|
0.8533237
|
0.8919444
|
0.9298658
|
0.9671133
|
1.0037127
|
1.0396900
|
1.0750716
|
1.1098841
|
1.1441543
|
1.177909
|
1.211176
|
1.243983
|
1.276356
|
1.308326
|
1.339918
|
1.371162
|
1.402086
|
1.432719
|
1.463089
|
1.493226
|
1.523159
|
1.552917
|
1.582530
|
1.6120274
|
1.6414388
|
1.6707944
|
1.7001242
|
1.7294585
|
|
Zeb2
|
-0.7180968
|
-0.7410789
|
-0.7637920
|
-0.7861678
|
-0.8081402
|
-0.8296457
|
-0.8506229
|
-0.8710128
|
-0.8907581
|
-0.9098038
|
-0.9280965
|
-0.9455843
|
-0.9622168
|
-0.9779447
|
-0.9927197
|
-1.0064942
|
-1.0192211
|
-1.0308534
|
-1.0413441
|
-1.0506457
|
-1.0587101
|
-1.0654881
|
-1.0709290
|
-1.0749806
|
-1.0775882
|
-1.0786947
|
-1.0782402
|
-1.0761611
|
-1.0723899
|
-1.0668549
|
-1.0594791
|
-1.0501804
|
-1.0388703
|
-1.0254538
|
-1.0098284
|
-0.9918835
|
-0.9714999
|
-0.9485487
|
-0.9228907
|
-0.8943754
|
-0.8628403
|
-0.8281098
|
-0.7899945
|
-0.7482966
|
-0.7029642
|
-0.6541077
|
-0.6018543
|
-0.5463430
|
-0.4877279
|
-0.4261797
|
-0.3618885
|
-0.2950656
|
-0.2259447
|
-0.1547834
|
-0.0818642
|
-0.0074949
|
0.0679911
|
0.1442351
|
0.2208534
|
0.2974382
|
0.3735591
|
0.4487640
|
0.5225817
|
0.5945233
|
0.6640846
|
0.7307491
|
0.7940291
|
0.8537544
|
0.9099226
|
0.9625474
|
1.0116557
|
1.0572871
|
1.0994927
|
1.1383342
|
1.1738831
|
1.2062196
|
1.2354319
|
1.2616158
|
1.2848734
|
1.3053128
|
1.3230474
|
1.338195
|
1.350879
|
1.361224
|
1.369360
|
1.375417
|
1.379532
|
1.381838
|
1.382475
|
1.381580
|
1.379293
|
1.375756
|
1.371108
|
1.365490
|
1.359044
|
1.3519102
|
1.3442293
|
1.3361413
|
1.3277859
|
1.3193019
|
|
Zfp276
|
-0.9059086
|
-0.9172381
|
-0.9284397
|
-0.9394636
|
-0.9502611
|
-0.9607851
|
-0.9709894
|
-0.9808291
|
-0.9902602
|
-0.9992398
|
-1.0077254
|
-1.0156754
|
-1.0230488
|
-1.0298045
|
-1.0359021
|
-1.0413007
|
-1.0459594
|
-1.0498369
|
-1.0528911
|
-1.0550792
|
-1.0563569
|
-1.0566790
|
-1.0559982
|
-1.0542653
|
-1.0514290
|
-1.0474349
|
-1.0422259
|
-1.0357414
|
-1.0279167
|
-1.0186829
|
-1.0079663
|
-0.9956877
|
-0.9817616
|
-0.9660963
|
-0.9485922
|
-0.9291417
|
-0.9076282
|
-0.8839248
|
-0.8578936
|
-0.8293845
|
-0.7982337
|
-0.7642625
|
-0.7272754
|
-0.6870646
|
-0.6435442
|
-0.5967682
|
-0.5468040
|
-0.4937295
|
-0.4376359
|
-0.3786301
|
-0.3168382
|
-0.2524079
|
-0.1855115
|
-0.1163484
|
-0.0451477
|
0.0278295
|
0.1022882
|
0.1778973
|
0.2542890
|
0.3310572
|
0.4077577
|
0.4839079
|
0.5589884
|
0.6324443
|
0.7036876
|
0.7721008
|
0.8370833
|
0.8983692
|
0.9558771
|
1.0095489
|
1.0593471
|
1.1052551
|
1.1472762
|
1.1854326
|
1.2197645
|
1.2503292
|
1.2771999
|
1.3004649
|
1.3202257
|
1.3365966
|
1.3497030
|
1.359681
|
1.366674
|
1.370834
|
1.372322
|
1.371300
|
1.367939
|
1.362409
|
1.354888
|
1.345551
|
1.334577
|
1.322143
|
1.308429
|
1.293611
|
1.277865
|
1.2613647
|
1.2442824
|
1.2267874
|
1.2090464
|
1.1912235
|
write.table(heatmap_matrix_q_value_5_10_minus_5, file = file.path(tables_directory, "1-hindbrain_oligodendrocytes_joint_pons_clusters_14_4_8_21-significant_transcription_factors_diff_test_analysis_qval_5_10_minus_5_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)
Ordered pseudotime heatmap (Sam’s function)
ordered_matrix <- ordered_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], show_rownames=FALSE, return_matrix = FALSE)

ordered_matrix <- ordered_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], show_rownames=FALSE, return_matrix = FALSE)

ordered_matrix <- ordered_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], show_rownames=TRUE, return_matrix = TRUE)

ordered_matrix <- as.data.frame(ordered_matrix) %>% rownames_to_column("gene")
ordered_matrix <- left_join(select(transcription_factors_table_q_value_5_10_minus_5, gene, pval, qval, num_cells_expressed), ordered_matrix)
write.table(ordered_matrix, file = file.path(tables_directory, "1-hindbrain_oligodendrocytes_joint_pons_clusters_14_4_8_21_differential_gene_test_analysis_qval_5_10_minus_5_sam_ordered_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)
q value < 0.01
significant_genes_q_value_0.01 <- filter(diff_test_res_all_genes, qval < 0.01) %>% .$gene
cat("Number of significant genes: ", length(significant_genes_q_value_0.01))
## Number of significant genes: 6428
significant_transcription_factors_q_value_0.01 <- as.character(significant_genes_q_value_0.01[significant_genes_q_value_0.01 %in% transcription_factors$Symbol])
cat("Number of significant transcription factors:", length(significant_transcription_factors_q_value_0.01))
## Number of significant transcription factors: 428
plot_genes_heatmap_output_q_value_0.01 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_0.01,], cluster_rows=TRUE, num_clusters=1, return_heatmap=TRUE, show_rownames = TRUE)

save_pheatmap_pdf(plot_genes_heatmap_output_q_value_0.01[[2]], file.path("figures", "1-hindbrain_oligodendrocytes_joint_pons_clusters_14_4_8_21", "diff_test_plots_transcription_factors_only_q_value_0.01_heatmap_custom.pdf"), width=16, height=40)
## pdf
## 2
heatmap_matrix_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[1]]
ph_res_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[2]]
pheatmap_ordering_q_value_0.01 <- rownames(heatmap_matrix_q_value_0.01[ph_res_q_value_0.01$tree_row[["order"]],])
transcription_factors_table_q_value_0.01 <- filter(diff_test_res_all_genes, gene %in% significant_transcription_factors_q_value_0.01)
# Put genes from the transcription factor table in the same order
transcription_factors_table_q_value_0.01 <- transcription_factors_table_q_value_0.01 %>% arrange(match(gene, pheatmap_ordering_q_value_0.01))
write.table(transcription_factors_table_q_value_0.01, file.path(tables_directory, "1-hindbrain_oligodendrocytes_joint_pons_clusters_14_4_8_21-significant_transcription_factors_diff_test_analysis_qval_0.01.txt"), sep="\t", quote=FALSE, row.names=FALSE)
heatmap_matrix_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[1]]
heatmap_matrix_q_value_0.01 <- as.data.frame(heatmap_matrix_q_value_0.01) %>% rownames_to_column("gene")
heatmap_matrix_q_value_0.01 <- heatmap_matrix_q_value_0.01 %>% arrange(match(gene, pheatmap_ordering_q_value_0.01))
heatmap_matrix_q_value_0.01 %>% head(20) %>% kable() %>% kable_styling() %>% scroll_box(height="200px", width="600px")
|
gene
|
1
|
2
|
3
|
4
|
5
|
6
|
7
|
8
|
9
|
10
|
11
|
12
|
13
|
14
|
15
|
16
|
17
|
18
|
19
|
20
|
21
|
22
|
23
|
24
|
25
|
26
|
27
|
28
|
29
|
30
|
31
|
32
|
33
|
34
|
35
|
36
|
37
|
38
|
39
|
40
|
41
|
42
|
43
|
44
|
45
|
46
|
47
|
48
|
49
|
50
|
51
|
52
|
53
|
54
|
55
|
56
|
57
|
58
|
59
|
60
|
61
|
62
|
63
|
64
|
65
|
66
|
67
|
68
|
69
|
70
|
71
|
72
|
73
|
74
|
75
|
76
|
77
|
78
|
79
|
80
|
81
|
82
|
83
|
84
|
85
|
86
|
87
|
88
|
89
|
90
|
91
|
92
|
93
|
94
|
95
|
96
|
97
|
98
|
99
|
100
|
|
Zkscan1
|
-2.3515088
|
-2.2867933
|
-2.2213874
|
-2.1553217
|
-2.0886285
|
-2.0213417
|
-1.9534967
|
-1.8851308
|
-1.8162828
|
-1.7469932
|
-1.6773043
|
-1.6072600
|
-1.5369059
|
-1.4662894
|
-1.3954596
|
-1.3244672
|
-1.2533647
|
-1.1822062
|
-1.1110476
|
-1.0399464
|
-0.9689616
|
-0.8981540
|
-0.8275857
|
-0.7573205
|
-0.6874238
|
-0.6179622
|
-0.5490038
|
-0.4806181
|
-0.4128757
|
-0.3458487
|
-0.2796101
|
-0.2142342
|
-0.1497961
|
-0.0863721
|
-0.0240392
|
0.0371249
|
0.0970416
|
0.1556318
|
0.2128160
|
0.2685141
|
0.3226458
|
0.3751307
|
0.4258881
|
0.4748383
|
0.5219180
|
0.5670820
|
0.6102866
|
0.6514890
|
0.6906476
|
0.7277220
|
0.7626730
|
0.7954622
|
0.8260531
|
0.8544099
|
0.8804984
|
0.9042860
|
0.9257411
|
0.9448340
|
0.9615361
|
0.9758207
|
0.9876625
|
0.9970380
|
1.0039252
|
1.0083040
|
1.0101559
|
1.0094643
|
1.0062213
|
1.0004773
|
0.9923120
|
0.9818066
|
0.9690438
|
0.9541073
|
0.9370819
|
0.9180530
|
0.8971068
|
0.8743300
|
0.8498096
|
0.8236329
|
0.7958872
|
0.7666599
|
0.7360382
|
0.7041089
|
0.6709587
|
0.6366736
|
0.6013392
|
0.5650403
|
0.5278612
|
0.4898850
|
0.4511944
|
0.4118708
|
0.3719947
|
0.3316457
|
0.2909020
|
0.2498409
|
0.2085385
|
0.1670696
|
0.1255078
|
0.0839255
|
0.0423939
|
0.0009829
|
|
Tcf25
|
-2.0686885
|
-2.0166078
|
-1.9643685
|
-1.9119697
|
-1.8594107
|
-1.8066909
|
-1.7538093
|
-1.7007653
|
-1.6475582
|
-1.5941871
|
-1.5406512
|
-1.4869498
|
-1.4330822
|
-1.3790474
|
-1.3248448
|
-1.2704735
|
-1.2159327
|
-1.1612216
|
-1.1063394
|
-1.0512853
|
-0.9960584
|
-0.9406580
|
-0.8850831
|
-0.8293329
|
-0.7734066
|
-0.7173034
|
-0.6610223
|
-0.6045626
|
-0.5479233
|
-0.4911035
|
-0.4341025
|
-0.3769192
|
-0.3195529
|
-0.2620025
|
-0.2042673
|
-0.1463463
|
-0.0882386
|
-0.0299433
|
0.0285406
|
0.0872139
|
0.1460777
|
0.2051327
|
0.2643801
|
0.3238164
|
0.3833340
|
0.4427179
|
0.5017458
|
0.5601929
|
0.6178324
|
0.6744349
|
0.7297693
|
0.7836021
|
0.8356982
|
0.8858208
|
0.9337316
|
0.9791912
|
1.0219589
|
1.0617935
|
1.0984533
|
1.1316965
|
1.1612814
|
1.1869669
|
1.2085129
|
1.2256805
|
1.2382327
|
1.2459345
|
1.2485826
|
1.2462116
|
1.2389742
|
1.2270272
|
1.2105296
|
1.1896430
|
1.1645310
|
1.1353589
|
1.1022934
|
1.0655026
|
1.0251553
|
0.9814213
|
0.9344707
|
0.8844736
|
0.8316007
|
0.7760219
|
0.7179071
|
0.6574256
|
0.5947459
|
0.5300354
|
0.4634607
|
0.3951872
|
0.3253788
|
0.2541979
|
0.1818056
|
0.1083609
|
0.0340213
|
-0.0410575
|
-0.1167220
|
-0.1928205
|
-0.2692035
|
-0.3457234
|
-0.4222350
|
-0.4985949
|
|
Mxd4
|
-2.4702821
|
-2.4059614
|
-2.3401159
|
-2.2727727
|
-2.2039639
|
-2.1337271
|
-2.0621056
|
-1.9891483
|
-1.9149102
|
-1.8394525
|
-1.7628427
|
-1.6851547
|
-1.6064690
|
-1.5268730
|
-1.4464607
|
-1.3653327
|
-1.2835966
|
-1.2013669
|
-1.1187645
|
-1.0359171
|
-0.9529591
|
-0.8700310
|
-0.7872795
|
-0.7048575
|
-0.6229234
|
-0.5416410
|
-0.4611795
|
-0.3817125
|
-0.3034183
|
-0.2264788
|
-0.1510797
|
-0.0774097
|
-0.0056598
|
0.0639768
|
0.1313054
|
0.1961307
|
0.2582568
|
0.3174886
|
0.3736317
|
0.4264934
|
0.4758835
|
0.5216148
|
0.5635039
|
0.6013779
|
0.6352150
|
0.6651509
|
0.6913389
|
0.7139418
|
0.7331311
|
0.7490859
|
0.7619920
|
0.7720408
|
0.7794286
|
0.7843559
|
0.7870263
|
0.7876463
|
0.7864242
|
0.7835696
|
0.7792932
|
0.7738061
|
0.7673194
|
0.7600440
|
0.7521902
|
0.7439675
|
0.7355846
|
0.7272492
|
0.7191519
|
0.7113486
|
0.7038304
|
0.6965876
|
0.6896109
|
0.6828908
|
0.6764180
|
0.6701832
|
0.6641772
|
0.6583909
|
0.6528151
|
0.6474408
|
0.6422589
|
0.6372605
|
0.6324367
|
0.6277785
|
0.6232770
|
0.6189234
|
0.6147090
|
0.6106250
|
0.6066626
|
0.6028131
|
0.5990677
|
0.5954180
|
0.5918551
|
0.5883705
|
0.5849556
|
0.5816017
|
0.5783004
|
0.5750431
|
0.5718212
|
0.5686262
|
0.5654497
|
0.5622831
|
|
Sox4
|
-2.3108759
|
-2.2496594
|
-2.1877902
|
-2.1253049
|
-2.0622417
|
-1.9986405
|
-1.9345429
|
-1.8699918
|
-1.8050321
|
-1.7397101
|
-1.6740734
|
-1.6081714
|
-1.5420548
|
-1.4757756
|
-1.4093872
|
-1.3429444
|
-1.2765031
|
-1.2101204
|
-1.1438546
|
-1.0777649
|
-1.0119118
|
-0.9463565
|
-0.8811612
|
-0.8163888
|
-0.7521030
|
-0.6883683
|
-0.6252497
|
-0.5628129
|
-0.5011240
|
-0.4402495
|
-0.3802564
|
-0.3212119
|
-0.2631836
|
-0.2062391
|
-0.1504462
|
-0.0958728
|
-0.0425869
|
0.0093439
|
0.0598517
|
0.1088691
|
0.1563286
|
0.2021632
|
0.2463064
|
0.2886934
|
0.3293009
|
0.3681482
|
0.4052581
|
0.4406545
|
0.4743631
|
0.5064104
|
0.5368245
|
0.5656343
|
0.5928700
|
0.6185627
|
0.6427444
|
0.6654479
|
0.6867071
|
0.7065564
|
0.7250309
|
0.7421667
|
0.7580001
|
0.7725683
|
0.7859088
|
0.7980597
|
0.8090597
|
0.8189475
|
0.8277619
|
0.8355356
|
0.8422987
|
0.8480814
|
0.8529145
|
0.8568286
|
0.8598549
|
0.8620244
|
0.8633686
|
0.8639191
|
0.8637074
|
0.8627654
|
0.8611249
|
0.8588180
|
0.8558766
|
0.8523330
|
0.8482191
|
0.8435674
|
0.8384098
|
0.8327788
|
0.8267064
|
0.8202249
|
0.8133665
|
0.8061634
|
0.7986477
|
0.7908515
|
0.7828068
|
0.7745456
|
0.7660999
|
0.7575015
|
0.7487822
|
0.7399737
|
0.7311077
|
0.7222157
|
|
Mycl
|
-0.8139043
|
-0.8356217
|
-0.8570808
|
-0.8781969
|
-0.8988877
|
-0.9190737
|
-0.9386780
|
-0.9576256
|
-0.9758441
|
-0.9932627
|
-1.0098125
|
-1.0254258
|
-1.0400364
|
-1.0535788
|
-1.0659880
|
-1.0771995
|
-1.0871484
|
-1.0957695
|
-1.1029965
|
-1.1087619
|
-1.1129964
|
-1.1156284
|
-1.1165834
|
-1.1157837
|
-1.1131477
|
-1.1085892
|
-1.1020169
|
-1.0933336
|
-1.0824355
|
-1.0692114
|
-1.0535420
|
-1.0352986
|
-1.0143426
|
-0.9905241
|
-0.9636813
|
-0.9336384
|
-0.9002053
|
-0.8631758
|
-0.8223259
|
-0.7774128
|
-0.7281729
|
-0.6743200
|
-0.6155438
|
-0.5515192
|
-0.4821733
|
-0.4077212
|
-0.3284172
|
-0.2445489
|
-0.1564421
|
-0.0644661
|
0.0309624
|
0.1293757
|
0.2302525
|
0.3330160
|
0.4370333
|
0.5416155
|
0.6460186
|
0.7494465
|
0.8510536
|
0.9499494
|
1.0452041
|
1.1358542
|
1.2209101
|
1.2993640
|
1.3701986
|
1.4323966
|
1.4850304
|
1.5278494
|
1.5609704
|
1.5845620
|
1.5988387
|
1.6040561
|
1.6005069
|
1.5885170
|
1.5684413
|
1.5406606
|
1.5055775
|
1.4636133
|
1.4152045
|
1.3607999
|
1.3008575
|
1.2358413
|
1.1662188
|
1.0924581
|
1.0150253
|
0.9343821
|
0.8509834
|
0.7652750
|
0.6776917
|
0.5886550
|
0.4985718
|
0.4078323
|
0.3168090
|
0.2258555
|
0.1353050
|
0.0454702
|
-0.0433578
|
-0.1309095
|
-0.2169374
|
-0.3012157
|
|
Zfp809
|
-1.3034221
|
-1.2958219
|
-1.2881296
|
-1.2803221
|
-1.2723759
|
-1.2642664
|
-1.2559680
|
-1.2474542
|
-1.2386977
|
-1.2296698
|
-1.2203409
|
-1.2106801
|
-1.2006551
|
-1.1902322
|
-1.1793763
|
-1.1680504
|
-1.1562159
|
-1.1438322
|
-1.1308565
|
-1.1172436
|
-1.1029460
|
-1.0879132
|
-1.0720919
|
-1.0554255
|
-1.0378535
|
-1.0193120
|
-0.9997324
|
-0.9790415
|
-0.9571613
|
-0.9340078
|
-0.9094910
|
-0.8835142
|
-0.8559734
|
-0.8267563
|
-0.7957420
|
-0.7627996
|
-0.7277877
|
-0.6905529
|
-0.6509291
|
-0.6087355
|
-0.5637761
|
-0.5158371
|
-0.4646857
|
-0.4100742
|
-0.3518881
|
-0.2901735
|
-0.2250053
|
-0.1564849
|
-0.0847443
|
-0.0099508
|
0.0676884
|
0.1479223
|
0.2304514
|
0.3149246
|
0.4009352
|
0.4880187
|
0.5756506
|
0.6632457
|
0.7501580
|
0.8356825
|
0.9190582
|
0.9994720
|
1.0760662
|
1.1479455
|
1.2141879
|
1.2738564
|
1.3260735
|
1.3704829
|
1.4070306
|
1.4357279
|
1.4566478
|
1.4699204
|
1.4757293
|
1.4743068
|
1.4659285
|
1.4509085
|
1.4295937
|
1.4023585
|
1.3695993
|
1.3317295
|
1.2891742
|
1.2423656
|
1.1917382
|
1.1377253
|
1.0807546
|
1.0212450
|
0.9596041
|
0.8962250
|
0.8314846
|
0.7657416
|
0.6993355
|
0.6325851
|
0.5657882
|
0.4992210
|
0.4331382
|
0.3677731
|
0.3033378
|
0.2400242
|
0.1780042
|
0.1174311
|
|
Hif1a
|
-0.3962246
|
-0.4416984
|
-0.4867114
|
-0.5311344
|
-0.5748421
|
-0.6177130
|
-0.6596289
|
-0.7004752
|
-0.7401405
|
-0.7785164
|
-0.8154974
|
-0.8509803
|
-0.8848643
|
-0.9170506
|
-0.9474418
|
-0.9759420
|
-1.0024560
|
-1.0268890
|
-1.0491466
|
-1.0691335
|
-1.0867540
|
-1.1019108
|
-1.1145047
|
-1.1244341
|
-1.1315946
|
-1.1358778
|
-1.1371715
|
-1.1353584
|
-1.1303155
|
-1.1219136
|
-1.1100165
|
-1.0944800
|
-1.0751511
|
-1.0518673
|
-1.0244552
|
-0.9927300
|
-0.9564943
|
-0.9155368
|
-0.8696312
|
-0.8185352
|
-0.7619888
|
-0.6997133
|
-0.6314097
|
-0.5567727
|
-0.4758483
|
-0.3890663
|
-0.2968956
|
-0.1998325
|
-0.0984055
|
0.0068214
|
0.1152451
|
0.2262212
|
0.3390618
|
0.4530350
|
0.5673641
|
0.6812284
|
0.7937644
|
0.9040680
|
1.0111974
|
1.1141771
|
1.2120022
|
1.3036439
|
1.3880557
|
1.4641802
|
1.5309570
|
1.5873308
|
1.6323521
|
1.6658479
|
1.6880540
|
1.6992512
|
1.6997592
|
1.6899327
|
1.6701572
|
1.6408462
|
1.6024371
|
1.5553878
|
1.5001742
|
1.4372860
|
1.3672246
|
1.2904995
|
1.2076262
|
1.1191228
|
1.0255078
|
0.9272976
|
0.8250042
|
0.7191327
|
0.6101798
|
0.4986311
|
0.3849599
|
0.2696254
|
0.1530710
|
0.0357232
|
-0.0820095
|
-0.1997379
|
-0.3170925
|
-0.4337244
|
-0.5493056
|
-0.6635294
|
-0.7761102
|
-0.8867837
|
|
Hmg20b
|
-0.1945130
|
-0.2543854
|
-0.3136301
|
-0.3721075
|
-0.4296825
|
-0.4862246
|
-0.5416075
|
-0.5957090
|
-0.6484108
|
-0.6995982
|
-0.7491600
|
-0.7969880
|
-0.8429768
|
-0.8870234
|
-0.9290272
|
-0.9688890
|
-1.0065113
|
-1.0417975
|
-1.0746514
|
-1.1049772
|
-1.1326787
|
-1.1576589
|
-1.1798194
|
-1.1990603
|
-1.2152791
|
-1.2283706
|
-1.2382259
|
-1.2447321
|
-1.2477717
|
-1.2472215
|
-1.2429524
|
-1.2348281
|
-1.2227049
|
-1.2064301
|
-1.1858419
|
-1.1607679
|
-1.1310242
|
-1.0964144
|
-1.0567282
|
-1.0117406
|
-0.9612101
|
-0.9048773
|
-0.8424637
|
-0.7736845
|
-0.6985871
|
-0.6175776
|
-0.5310916
|
-0.4395830
|
-0.3435273
|
-0.2434260
|
-0.1398097
|
-0.0332408
|
0.0756840
|
0.1863317
|
0.2980314
|
0.4100739
|
0.5217112
|
0.6321570
|
0.7405878
|
0.8461449
|
0.9479367
|
1.0450428
|
1.1365173
|
1.2213947
|
1.2986956
|
1.3674330
|
1.4267031
|
1.4762919
|
1.5163489
|
1.5470597
|
1.5686421
|
1.5813426
|
1.5854345
|
1.5812147
|
1.5690013
|
1.5491311
|
1.5219568
|
1.4878448
|
1.4471725
|
1.4003263
|
1.3476992
|
1.2896886
|
1.2266947
|
1.1591181
|
1.0873583
|
1.0118121
|
0.9328719
|
0.8509246
|
0.7663500
|
0.6795201
|
0.5907975
|
0.5005351
|
0.4090752
|
0.3167489
|
0.2238752
|
0.1307614
|
0.0377022
|
-0.0550202
|
-0.1471362
|
-0.2383887
|
|
Atf6b
|
-0.2376819
|
-0.2951443
|
-0.3520373
|
-0.4082242
|
-0.4635723
|
-0.5179530
|
-0.5712416
|
-0.6233173
|
-0.6740626
|
-0.7233634
|
-0.7711090
|
-0.8171912
|
-0.8615045
|
-0.9039458
|
-0.9444138
|
-0.9828091
|
-1.0190334
|
-1.0529895
|
-1.0845805
|
-1.1137099
|
-1.1402807
|
-1.1641955
|
-1.1853554
|
-1.2036600
|
-1.2190067
|
-1.2312901
|
-1.2404017
|
-1.2462289
|
-1.2486551
|
-1.2475581
|
-1.2428103
|
-1.2342774
|
-1.2218181
|
-1.2052828
|
-1.1845135
|
-1.1593420
|
-1.1295897
|
-1.0950664
|
-1.0555690
|
-1.0108809
|
-0.9607701
|
-0.9049887
|
-0.8432710
|
-0.7753467
|
-0.7012697
|
-0.6214432
|
-0.5362991
|
-0.4462861
|
-0.3518735
|
-0.2535547
|
-0.1518499
|
-0.0473088
|
0.0594877
|
0.1679256
|
0.2773566
|
0.3870977
|
0.4964312
|
0.6046050
|
0.7108342
|
0.8143021
|
0.9141633
|
1.0095467
|
1.0995588
|
1.1832886
|
1.2598123
|
1.3281996
|
1.3875982
|
1.4378123
|
1.4789889
|
1.5113074
|
1.5349745
|
1.5502220
|
1.5573049
|
1.5564985
|
1.5480968
|
1.5324098
|
1.5097617
|
1.4804887
|
1.4449368
|
1.4034603
|
1.3564198
|
1.3041801
|
1.2471089
|
1.1855752
|
1.1199475
|
1.0505929
|
0.9778752
|
0.9021542
|
0.8237844
|
0.7431139
|
0.6604838
|
0.5762273
|
0.4906686
|
0.4041230
|
0.3168959
|
0.2292827
|
0.1415683
|
0.0540270
|
-0.0330777
|
-0.1194930
|
|
Xpa
|
-1.7642787
|
-1.7247771
|
-1.6848583
|
-1.6445148
|
-1.6037387
|
-1.5625222
|
-1.5208571
|
-1.4787351
|
-1.4361478
|
-1.3930864
|
-1.3495421
|
-1.3055058
|
-1.2609680
|
-1.2159194
|
-1.1703502
|
-1.1242505
|
-1.0776099
|
-1.0304183
|
-0.9826648
|
-0.9343387
|
-0.8854288
|
-0.8359237
|
-0.7858118
|
-0.7350813
|
-0.6837200
|
-0.6317154
|
-0.5790550
|
-0.5257256
|
-0.4717142
|
-0.4170072
|
-0.3615907
|
-0.3054506
|
-0.2485725
|
-0.1909416
|
-0.1325429
|
-0.0733609
|
-0.0133800
|
0.0474159
|
0.1090432
|
0.1715186
|
0.2348593
|
0.2990828
|
0.3642069
|
0.4302435
|
0.4970532
|
0.5643342
|
0.6317648
|
0.6990103
|
0.7657228
|
0.8315415
|
0.8960935
|
0.9589942
|
1.0198479
|
1.0782494
|
1.1337848
|
1.1860328
|
1.2345672
|
1.2789576
|
1.3187726
|
1.3535811
|
1.3829555
|
1.4064740
|
1.4237235
|
1.4343029
|
1.4378258
|
1.4339241
|
1.4222961
|
1.4030296
|
1.3764124
|
1.3427524
|
1.3023736
|
1.2556138
|
1.2028220
|
1.1443564
|
1.0805820
|
1.0118685
|
0.9385882
|
0.8611139
|
0.7798174
|
0.6950674
|
0.6072283
|
0.5166583
|
0.4237082
|
0.3287202
|
0.2320268
|
0.1339497
|
0.0347992
|
-0.0651270
|
-0.1655437
|
-0.2661795
|
-0.3667764
|
-0.4670906
|
-0.5668925
|
-0.6659665
|
-0.7641115
|
-0.8611402
|
-0.9568791
|
-1.0511685
|
-1.1438616
|
-1.2348247
|
|
Xbp1
|
-1.6987856
|
-1.6575967
|
-1.6160776
|
-1.5742199
|
-1.5320153
|
-1.4894551
|
-1.4465305
|
-1.4032324
|
-1.3595517
|
-1.3154787
|
-1.2710039
|
-1.2261174
|
-1.1808090
|
-1.1350685
|
-1.0888851
|
-1.0422482
|
-0.9951467
|
-0.9475694
|
-0.8995046
|
-0.8509408
|
-0.8018658
|
-0.7522674
|
-0.7021331
|
-0.6514501
|
-0.6002054
|
-0.5483856
|
-0.4959771
|
-0.4429661
|
-0.3893385
|
-0.3350797
|
-0.2801750
|
-0.2246094
|
-0.1683676
|
-0.1114338
|
-0.0537921
|
0.0045737
|
0.0636804
|
0.1235448
|
0.1841843
|
0.2456164
|
0.3078592
|
0.3709310
|
0.4348505
|
0.4996299
|
0.5651170
|
0.6309852
|
0.6968898
|
0.7624755
|
0.8273761
|
0.8912156
|
0.9536078
|
1.0141577
|
1.0724615
|
1.1281082
|
1.1806803
|
1.2297553
|
1.2749068
|
1.3157066
|
1.3517257
|
1.3825370
|
1.4077168
|
1.4268473
|
1.4395187
|
1.4453320
|
1.4439014
|
1.4348573
|
1.4178950
|
1.3931090
|
1.3607960
|
1.3212696
|
1.2748564
|
1.2218942
|
1.1627302
|
1.0977189
|
1.0272208
|
0.9516001
|
0.8712233
|
0.7864577
|
0.6976696
|
0.6052232
|
0.5094790
|
0.4107927
|
0.3095138
|
0.2059848
|
0.1005398
|
-0.0064959
|
-0.1148071
|
-0.2240891
|
-0.3340486
|
-0.4444039
|
-0.5548858
|
-0.6652373
|
-0.7752147
|
-0.8845870
|
-0.9931365
|
-1.1006586
|
-1.2069618
|
-1.3118675
|
-1.4152101
|
-1.5168362
|
|
Nkx2-2
|
-0.0138960
|
-0.0719516
|
-0.1290422
|
-0.1850259
|
-0.2397697
|
-0.2931491
|
-0.3450476
|
-0.3953569
|
-0.4439760
|
-0.4908108
|
-0.5357738
|
-0.5787834
|
-0.6197628
|
-0.6586404
|
-0.6953478
|
-0.7298202
|
-0.7619948
|
-0.7918103
|
-0.8192061
|
-0.8441214
|
-0.8664939
|
-0.8862594
|
-0.9033505
|
-0.9176957
|
-0.9292179
|
-0.9378340
|
-0.9434531
|
-0.9459754
|
-0.9452910
|
-0.9412786
|
-0.9338037
|
-0.9227173
|
-0.9078538
|
-0.8890300
|
-0.8660424
|
-0.8386654
|
-0.8066495
|
-0.7697182
|
-0.7275665
|
-0.6798574
|
-0.6262199
|
-0.5662457
|
-0.4994865
|
-0.4254684
|
-0.3440988
|
-0.2557248
|
-0.1607588
|
-0.0596711
|
0.0470004
|
0.1586416
|
0.2745562
|
0.3939607
|
0.5159821
|
0.6396572
|
0.7639348
|
0.8876788
|
1.0096744
|
1.1286355
|
1.2432141
|
1.3520111
|
1.4535881
|
1.5464812
|
1.6292145
|
1.7003161
|
1.7583342
|
1.8018538
|
1.8296376
|
1.8415190
|
1.8379103
|
1.8193148
|
1.7863146
|
1.7395623
|
1.6797741
|
1.6077224
|
1.5242290
|
1.4301588
|
1.3264133
|
1.2139237
|
1.0936449
|
0.9665481
|
0.8336139
|
0.6958249
|
0.5541582
|
0.4095775
|
0.2630253
|
0.1154148
|
-0.0323774
|
-0.1795193
|
-0.3252300
|
-0.4687863
|
-0.6095277
|
-0.7468612
|
-0.8802645
|
-1.0092875
|
-1.1335539
|
-1.2527598
|
-1.3666724
|
-1.4751270
|
-1.5780226
|
-1.6753178
|
|
Son
|
-0.2791494
|
-0.3271638
|
-0.3749621
|
-0.4223987
|
-0.4693291
|
-0.5156097
|
-0.5610975
|
-0.6056504
|
-0.6491271
|
-0.6913869
|
-0.7322900
|
-0.7716969
|
-0.8094689
|
-0.8454678
|
-0.8795555
|
-0.9115946
|
-0.9414478
|
-0.9689779
|
-0.9940478
|
-1.0165202
|
-1.0362578
|
-1.0531228
|
-1.0669770
|
-1.0776817
|
-1.0850973
|
-1.0890834
|
-1.0894986
|
-1.0862001
|
-1.0790439
|
-1.0678843
|
-1.0525739
|
-1.0329633
|
-1.0089011
|
-0.9802334
|
-0.9468040
|
-0.9084536
|
-0.8650204
|
-0.8163391
|
-0.7622412
|
-0.7025546
|
-0.6371035
|
-0.5657079
|
-0.4881838
|
-0.4043606
|
-0.3144901
|
-0.2192615
|
-0.1193895
|
-0.0155967
|
0.0913862
|
0.2008196
|
0.3119543
|
0.4240314
|
0.5362824
|
0.6479289
|
0.7581832
|
0.8662484
|
0.9713192
|
1.0725824
|
1.1692180
|
1.2604000
|
1.3452976
|
1.4230765
|
1.4929001
|
1.5539315
|
1.6053346
|
1.6462763
|
1.6760144
|
1.6945180
|
1.7021106
|
1.6991270
|
1.6859108
|
1.6628128
|
1.6301907
|
1.5884081
|
1.5378336
|
1.4788405
|
1.4118057
|
1.3371093
|
1.2551338
|
1.1662637
|
1.0708847
|
0.9693832
|
0.8621460
|
0.7495593
|
0.6320086
|
0.5098782
|
0.3835503
|
0.2534050
|
0.1198197
|
-0.0168312
|
-0.1561771
|
-0.2978511
|
-0.4414906
|
-0.5867377
|
-0.7332392
|
-0.8806474
|
-1.0286199
|
-1.1768200
|
-1.3249170
|
-1.4725862
|
|
Sox8
|
-0.5141742
|
-0.5439075
|
-0.5733761
|
-0.6024667
|
-0.6310684
|
-0.6590726
|
-0.6863728
|
-0.7128645
|
-0.7384452
|
-0.7630142
|
-0.7864723
|
-0.8087217
|
-0.8296657
|
-0.8492088
|
-0.8672559
|
-0.8837125
|
-0.8984839
|
-0.9114755
|
-0.9225918
|
-0.9317365
|
-0.9388119
|
-0.9437185
|
-0.9463546
|
-0.9466156
|
-0.9443941
|
-0.9395788
|
-0.9320540
|
-0.9216996
|
-0.9083899
|
-0.8919931
|
-0.8723712
|
-0.8493785
|
-0.8228615
|
-0.7926582
|
-0.7585969
|
-0.7204958
|
-0.6781623
|
-0.6313921
|
-0.5799680
|
-0.5236597
|
-0.4622226
|
-0.3953972
|
-0.3229079
|
-0.2444787
|
-0.1602059
|
-0.0705917
|
0.0238155
|
0.1224337
|
0.2246448
|
0.3297914
|
0.4371754
|
0.5460574
|
0.6556559
|
0.7651492
|
0.8736760
|
0.9803381
|
1.0842038
|
1.1843108
|
1.2796713
|
1.3692762
|
1.4521010
|
1.5271118
|
1.5932710
|
1.6495450
|
1.6949113
|
1.7283663
|
1.7490295
|
1.7568367
|
1.7521493
|
1.7353726
|
1.7069491
|
1.6673551
|
1.6170963
|
1.5567052
|
1.4867372
|
1.4077677
|
1.3203890
|
1.2252074
|
1.1228404
|
1.0139134
|
0.8990570
|
0.7789042
|
0.6540872
|
0.5252349
|
0.3929694
|
0.2579035
|
0.1206377
|
-0.0182427
|
-0.1581701
|
-0.2985978
|
-0.4390016
|
-0.5788831
|
-0.7177709
|
-0.8552231
|
-0.9908283
|
-1.1242073
|
-1.2550137
|
-1.3829349
|
-1.5076916
|
-1.6290383
|
|
Cebpz
|
-0.7058591
|
-0.7273201
|
-0.7486146
|
-0.7696388
|
-0.7902901
|
-0.8104669
|
-0.8300687
|
-0.8489962
|
-0.8671507
|
-0.8844345
|
-0.9007507
|
-0.9160026
|
-0.9300945
|
-0.9429304
|
-0.9544149
|
-0.9644522
|
-0.9729464
|
-0.9798012
|
-0.9849194
|
-0.9882032
|
-0.9895532
|
-0.9888689
|
-0.9860479
|
-0.9809859
|
-0.9735762
|
-0.9637093
|
-0.9512729
|
-0.9361513
|
-0.9182247
|
-0.8973695
|
-0.8734573
|
-0.8463546
|
-0.8159225
|
-0.7820159
|
-0.7444831
|
-0.7031655
|
-0.6578965
|
-0.6085013
|
-0.5547962
|
-0.4965875
|
-0.4336717
|
-0.3658335
|
-0.2928462
|
-0.2144853
|
-0.1308773
|
-0.0425259
|
0.0500284
|
0.1462220
|
0.2454653
|
0.3471403
|
0.4505996
|
0.5551643
|
0.6601243
|
0.7647373
|
0.8682298
|
0.9697980
|
1.0686095
|
1.1638053
|
1.2545031
|
1.3398003
|
1.4187788
|
1.4905090
|
1.5540560
|
1.6084850
|
1.6528682
|
1.6862922
|
1.7079527
|
1.7177890
|
1.7161268
|
1.7033302
|
1.6797958
|
1.6459490
|
1.6022404
|
1.5491426
|
1.4871465
|
1.4167584
|
1.3384966
|
1.2528883
|
1.1604669
|
1.0617689
|
0.9573317
|
0.8476904
|
0.7333760
|
0.6149128
|
0.4928165
|
0.3675922
|
0.2397325
|
0.1097162
|
-0.0219934
|
-0.1549497
|
-0.2887238
|
-0.4229056
|
-0.5571042
|
-0.6909489
|
-0.8240893
|
-0.9561958
|
-1.0869594
|
-1.2160921
|
-1.3433261
|
-1.4684140
|
|
Dmrtc1a
|
-1.3734099
|
-1.3591662
|
-1.3438435
|
-1.3273789
|
-1.3097093
|
-1.2907715
|
-1.2705033
|
-1.2488437
|
-1.2257343
|
-1.2011201
|
-1.1749504
|
-1.1471803
|
-1.1177716
|
-1.0866945
|
-1.0539292
|
-1.0194667
|
-0.9833115
|
-0.9454822
|
-0.9060139
|
-0.8649595
|
-0.8223913
|
-0.7784025
|
-0.7331087
|
-0.6866489
|
-0.6391867
|
-0.5909107
|
-0.5420351
|
-0.4927995
|
-0.4434687
|
-0.3943315
|
-0.3456999
|
-0.2979063
|
-0.2513018
|
-0.2062528
|
-0.1631374
|
-0.1223414
|
-0.0842538
|
-0.0492611
|
-0.0177426
|
0.0099359
|
0.0334281
|
0.0524131
|
0.0666016
|
0.0757532
|
0.0799422
|
0.0795670
|
0.0750783
|
0.0669551
|
0.0556935
|
0.0417973
|
0.0257697
|
0.0081060
|
-0.0107114
|
-0.0302174
|
-0.0499669
|
-0.0695357
|
-0.0885210
|
-0.1065404
|
-0.1232295
|
-0.1382394
|
-0.1512323
|
-0.1618773
|
-0.1698445
|
-0.1747991
|
-0.1763933
|
-0.1742590
|
-0.1680357
|
-0.1576389
|
-0.1431025
|
-0.1244291
|
-0.1015917
|
-0.0745346
|
-0.0431753
|
-0.0074049
|
0.0329105
|
0.0779298
|
0.1278358
|
0.1828353
|
0.2431586
|
0.3090590
|
0.3808127
|
0.4587185
|
0.5430970
|
0.6342904
|
0.7326615
|
0.8385928
|
0.9524852
|
1.0747568
|
1.2058405
|
1.3461822
|
1.4962377
|
1.6564699
|
1.8273442
|
2.0093252
|
2.2028707
|
2.4084264
|
2.6264194
|
2.8572512
|
3.0000000
|
3.0000000
|
|
Hbp1
|
-2.2416182
|
-2.1775526
|
-2.1123486
|
-2.0460563
|
-1.9787309
|
-1.9104325
|
-1.8412263
|
-1.7711827
|
-1.7003778
|
-1.6288928
|
-1.5568150
|
-1.4842369
|
-1.4112570
|
-1.3379795
|
-1.2645143
|
-1.1909771
|
-1.1174893
|
-1.0441776
|
-0.9711747
|
-0.8986182
|
-0.8266511
|
-0.7554214
|
-0.6850817
|
-0.6157892
|
-0.5477052
|
-0.4809949
|
-0.4158267
|
-0.3523725
|
-0.2908064
|
-0.2313048
|
-0.1740457
|
-0.1192083
|
-0.0669720
|
-0.0175165
|
0.0289795
|
0.0723386
|
0.1123855
|
0.1489475
|
0.1818556
|
0.2109451
|
0.2360561
|
0.2570346
|
0.2737332
|
0.2860215
|
0.2940073
|
0.2980424
|
0.2984976
|
0.2957507
|
0.2901834
|
0.2821807
|
0.2721284
|
0.2604123
|
0.2474171
|
0.2335252
|
0.2191163
|
0.2045671
|
0.1902507
|
0.1765369
|
0.1637925
|
0.1523815
|
0.1426661
|
0.1350073
|
0.1297660
|
0.1273045
|
0.1279880
|
0.1321861
|
0.1402382
|
0.1521899
|
0.1679462
|
0.1874172
|
0.2105178
|
0.2371678
|
0.2672909
|
0.3008141
|
0.3376675
|
0.3777835
|
0.4210962
|
0.4675411
|
0.5170547
|
0.5695737
|
0.6250347
|
0.6833741
|
0.7445269
|
0.8084270
|
0.8750063
|
0.9441948
|
1.0159196
|
1.0901049
|
1.1666715
|
1.2455367
|
1.3266133
|
1.4098101
|
1.4950310
|
1.5821748
|
1.6711353
|
1.7618003
|
1.8540520
|
1.9477666
|
2.0428139
|
2.1390573
|
|
Sp7
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341186
|
-0.4341184
|
-0.4341177
|
-0.4341139
|
-0.4340983
|
-0.4340400
|
-0.4338478
|
-0.4332892
|
-0.4318580
|
-0.4286043
|
-0.4220076
|
-0.4100274
|
-0.3904573
|
-0.3615970
|
-0.3230614
|
-0.2763889
|
-0.2251161
|
-0.1741941
|
-0.1289158
|
-0.0937410
|
-0.0714195
|
-0.0626496
|
-0.0662753
|
-0.0798458
|
-0.1002952
|
-0.1245412
|
-0.1498917
|
-0.1742366
|
-0.1960650
|
-0.2143656
|
-0.2285667
|
-0.2390056
|
-0.2462552
|
-0.2507196
|
-0.2526686
|
-0.2522620
|
-0.2495662
|
-0.2445636
|
-0.2371570
|
-0.2271689
|
-0.2143375
|
-0.1983075
|
-0.1786183
|
-0.1546861
|
-0.1257816
|
-0.0910020
|
-0.0492352
|
0.0008836
|
0.0610248
|
0.1332297
|
0.2199881
|
0.3243320
|
0.4499461
|
0.6012988
|
0.7837936
|
1.0039437
|
1.2695686
|
1.5900105
|
1.9763680
|
2.4417355
|
3.0000000
|
3.0000000
|
3.0000000
|
3.0000000
|
|
Onecut2
|
-0.2233659
|
-0.2323474
|
-0.2411131
|
-0.2496660
|
-0.2580093
|
-0.2661461
|
-0.2740799
|
-0.2818138
|
-0.2893513
|
-0.2966959
|
-0.3038509
|
-0.3108198
|
-0.3176061
|
-0.3242133
|
-0.3306449
|
-0.3369044
|
-0.3429953
|
-0.3489211
|
-0.3546852
|
-0.3602910
|
-0.3657421
|
-0.3710417
|
-0.3761933
|
-0.3812002
|
-0.3860657
|
-0.3907930
|
-0.3953853
|
-0.3998458
|
-0.4041777
|
-0.4083839
|
-0.4124676
|
-0.4164316
|
-0.4202789
|
-0.4240124
|
-0.4276349
|
-0.4311491
|
-0.4345578
|
-0.4378635
|
-0.4410689
|
-0.4441764
|
-0.4471886
|
-0.4501079
|
-0.4529366
|
-0.4556763
|
-0.4583136
|
-0.4608205
|
-0.4631709
|
-0.4653405
|
-0.4673062
|
-0.4690461
|
-0.4705392
|
-0.4717642
|
-0.4726996
|
-0.4733228
|
-0.4736094
|
-0.4735329
|
-0.4730632
|
-0.4721661
|
-0.4708024
|
-0.4689258
|
-0.4664824
|
-0.4634079
|
-0.4596263
|
-0.4550464
|
-0.4495589
|
-0.4430319
|
-0.4353112
|
-0.4262524
|
-0.4157037
|
-0.4034849
|
-0.3893833
|
-0.3731491
|
-0.3544900
|
-0.3330655
|
-0.3084791
|
-0.2802709
|
-0.2479083
|
-0.2107760
|
-0.1681651
|
-0.1192614
|
-0.0631324
|
0.0012848
|
0.0751967
|
0.1599645
|
0.2571142
|
0.3683433
|
0.4955223
|
0.6406905
|
0.8060431
|
0.9939072
|
1.2067068
|
1.4469125
|
1.7169788
|
2.0192664
|
2.3559555
|
2.7289507
|
3.0000000
|
3.0000000
|
3.0000000
|
3.0000000
|
|
Nkx6-2
|
-0.4381157
|
-0.4443818
|
-0.4504403
|
-0.4562878
|
-0.4619224
|
-0.4673428
|
-0.4725487
|
-0.4775405
|
-0.4823192
|
-0.4868865
|
-0.4912445
|
-0.4953956
|
-0.4993428
|
-0.5030889
|
-0.5066373
|
-0.5099913
|
-0.5131543
|
-0.5161298
|
-0.5189210
|
-0.5215311
|
-0.5239634
|
-0.5262206
|
-0.5283054
|
-0.5302202
|
-0.5319669
|
-0.5335472
|
-0.5349623
|
-0.5362131
|
-0.5372998
|
-0.5382220
|
-0.5389790
|
-0.5395690
|
-0.5399899
|
-0.5402386
|
-0.5403111
|
-0.5402025
|
-0.5399067
|
-0.5394168
|
-0.5387241
|
-0.5378188
|
-0.5366894
|
-0.5353227
|
-0.5337032
|
-0.5318135
|
-0.5296370
|
-0.5271576
|
-0.5243571
|
-0.5212145
|
-0.5177061
|
-0.5138046
|
-0.5094794
|
-0.5046960
|
-0.4994154
|
-0.4935940
|
-0.4871825
|
-0.4801261
|
-0.4723628
|
-0.4638236
|
-0.4544308
|
-0.4440974
|
-0.4327262
|
-0.4202078
|
-0.4064200
|
-0.3912256
|
-0.3744711
|
-0.3559843
|
-0.3355737
|
-0.3130360
|
-0.2881520
|
-0.2606802
|
-0.2303556
|
-0.1968876
|
-0.1599595
|
-0.1192262
|
-0.0743141
|
-0.0248199
|
0.0296894
|
0.0896758
|
0.1556299
|
0.2280682
|
0.3075304
|
0.3945753
|
0.4897758
|
0.5937118
|
0.7069629
|
0.8300987
|
0.9636694
|
1.1081939
|
1.2641489
|
1.4319566
|
1.6119735
|
1.8044794
|
2.0096683
|
2.2276403
|
2.4583967
|
2.7018369
|
2.9577581
|
3.0000000
|
3.0000000
|
3.0000000
|
write.table(heatmap_matrix_q_value_0.01, file = file.path(tables_directory, "1-hindbrain_oligodendrocytes_joint_pons_clusters_14_4_8_21-significant_transcription_factors_diff_test_analysis_qval_0.01_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)
Ordered pseudotime heatmap (Sam’s function)
ordered_matrix <- ordered_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_0.01,], show_rownames=FALSE, return_matrix = FALSE)

ordered_matrix <- ordered_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_0.01,], show_rownames=FALSE, return_matrix = FALSE)

ordered_matrix <- ordered_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_0.01,], show_rownames=TRUE, return_matrix = TRUE)

ordered_matrix <- as.data.frame(ordered_matrix) %>% rownames_to_column("gene")
ordered_matrix <- left_join(select(transcription_factors_table_q_value_0.01, gene, pval, qval, num_cells_expressed), ordered_matrix)
write.table(ordered_matrix, file = file.path(tables_directory, "1-hindbrain_oligodendrocytes_joint_pons_clusters_14_4_8_21_differential_gene_test_analysis_qval_0.01_sam_ordered_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)
Plotting of transcription factors differentially expressed in pseudotime
Top 10 differentially expressed genes (q value < 5*10^-5)
transcription_factors_table_q_value_5_10_minus_5_ordered_qval <- arrange(transcription_factors_table_q_value_5_10_minus_5, qval)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[1]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[2]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[3]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[4]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[5]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[6]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[7]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[8]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[9]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)

marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[10]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
